Modified mesh loses changes when leaving edit mode
Various Explanations for the behaviour.
Incomplete list follows.


Shape Keys.  If there are multiple Shape Keys present,  then you may end up editing a shape key whose influence is zero 0 or close to zero. Blinking eyes could be done with various animation techniques including shape keys.
Modifiers.  Shrink Wrap or Armature modifier can change the mesh shape. That is the purpose of such modifiers.  For example small edits might be completely dominated by a Shrink Wrap Modifier and thus not visible.